The deal, which will pay the veteran $800,000 and has been in the works for some time, was finalized Thursday night and approved by Major League Baseball on Friday.
"I'm thankful that I have an opportunity to come back and be a part of my hometown team," said Clark, who lives in Glendale, Ariz. "Lord willing, the 2009 season will end with us being the last team standing."
The desire to nab a World Series ring contributed to Clark's desire to play at least another season. The 14-year veteran will turn 37 in June.
Clark was a force off the bench for the D-backs in 2007 when they won a National League-best 90 games and advanced to the NL Championship Series. Clark hit .249 with 17 homers and 51 RBIs that year and was the one who came up with the team's rallying cry of "Anybody. Anytime."
"Any time you have the opportunity to reach the playoffs and come a series away from the World Series you feel like you have unfinished business," Clark said.
Clark was a key contributor for the D-backs from 2005 through 2007, but reluctantly left as a free agent last year and signed with the Padres after negotiations with Arizona broke down.
The D-backs re-acquired Clark last July and hit .206 in limited playing time. His best year with Arizona came in 2005 when he hit 30 homers and drove in 87 runs.
Clark is expected to serve mainly as a pinch-hitter in 2009, a role in which he has excelled in the past. In addition to the success he has had coming off the bench, his impact has also been felt in how he has helped some of the team's younger players adjust to doing so.
"Last year we just weren't as good in the last third of the game as we needed to be and there were probably a lot of reasons for that," D-backs GM Josh Byrnes said during last month's Winter Meetings. "One of them is that we didn't score enough late in the game and obviously Tony has a history of helping teams do a little more offensively late in games."
After a hot start in 2008, the D-backs tailed off and finished in second place, two games behind the Dodgers.
"I'm excited about the possibilities of this year's team," Clark said. "We have a young nucleus, but that young nucleus has three or four years under their belts now. They have the opportunity to put that together and accomplish something special. I am looking forward to being a part of it."
Steve Gilbert is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.